TMCC3

transmembrane and coiled-coil domain family 3, the group of MicroRNA protein coding host genes|Transmembrane and coiled-coil domain containing

Basic information

Region (hg38): 12:94567122-94650557

Links

ENSG00000057704 ∙ NCBI:57458 ∙ OMIM:617459 ∙ HGNC:29199 ∙ Uniprot:Q9ULS5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TMCC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TMCC3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			28		1	29
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	2

Variants in TMCC3

This is a list of pathogenic ClinVar variants found in the TMCC3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-94571494-A-G		not specified	Uncertain significance (Apr 08, 2023)
12-94571512-C-T		not specified	Uncertain significance (Apr 29, 2024)
12-94571632-T-C		not specified	Uncertain significance (Apr 13, 2023)
12-94571691-T-C		not specified	Uncertain significance (Jan 10, 2023)
12-94571712-C-T		not specified	Uncertain significance (May 07, 2024)
12-94571713-G-A		not specified	Uncertain significance (Jul 07, 2022)
12-94571720-G-T		Myoepithelial tumor	Uncertain significance (Nov 01, 2022)
12-94578407-G-A		not specified	Uncertain significance (Sep 12, 2023)
12-94578521-C-T		not specified	Uncertain significance (Jul 07, 2022)
12-94581784-G-A		not specified	Uncertain significance (Aug 04, 2023)
12-94581814-T-C		not specified	Uncertain significance (Jan 16, 2024)
12-94581884-T-C		not specified	Uncertain significance (Apr 06, 2023)
12-94581900-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
12-94581961-T-A		not specified	Uncertain significance (Sep 26, 2023)
12-94582015-T-C		not specified	Uncertain significance (Jan 16, 2024)
12-94582053-C-T			Benign (Aug 16, 2018)
12-94582075-A-G		not specified	Uncertain significance (Dec 07, 2021)
12-94582104-G-A			Benign (Aug 16, 2018)
12-94582110-A-C		not specified	Uncertain significance (May 21, 2024)
12-94582133-C-T		not specified	Uncertain significance (Feb 10, 2022)
12-94582168-C-A		not specified	Uncertain significance (Dec 06, 2022)
12-94582231-A-G		not specified	Uncertain significance (Sep 14, 2023)
12-94582237-G-A		not specified	Uncertain significance (Jun 10, 2022)
12-94582247-G-A		not specified	Uncertain significance (Jul 25, 2023)
12-94582258-T-C		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TMCC3	protein_coding	protein_coding	ENST00000261226	4	83439

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000274	0.934	125712	0	35	125747	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.923	231	274	0.843	0.0000163	3113
Missense in Polyphen		102	135.49	0.75284		1592
Synonymous	0.302	113	117	0.965	0.00000783	914
Loss of Function	1.70	10	17.7	0.564	0.00000105	207

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000270	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.785
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.13

Haploinsufficiency Scores

• pHI: 0.0962
• hipred: N
• hipred_score: 0.204
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.163

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tmcc3

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding